Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002100.1 Hibiscus syriacus cultivar Beakdansim tig00004297_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61713
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1020 original size:42 final size:42
Alignment explanation
Indices: 973--1054 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
963 GAGATTAAAG
* *
973 TAAATCCTTCGAATCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGAATCATCAGTAAGCCTTTCGAGCAAGATGCT
* *
1015 TAAATCCTTCGAGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TAAATCCTTCGAATCATCAGTAAGCCTTTCGAGCAAGATG
1055 ATAAGACCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
TAAATCCTTCGAATCATCAGTAAGCCTTTCGAGCAAGATGCT
Found at i:1237 original size:215 final size:221
Alignment explanation
Indices: 752--1317 Score: 749
Period size: 215 Copynumber: 2.6 Consensus size: 221
742 ATTTGTAAGA
* *
752 CCTTCGGGCCATCAGTAAGTCTTTCGAGAATTG-TGCTTAAATCCTTCAGGTCATCTGTAAGCCT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCA-TGATGCTTAAATCCTTCAGGTCATCTGTAAGCCT
** *
816 TTCGAGCAAGATGATAAGACCTTTGATCCATCCATAAGACCTTCAGTGCTGGATGTTTTGAACAT
65 TTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGA-CTTCAGTGCTGGATGTTTTCAACAT
* * * *
881 TTTCGTTACTTGATTCATGACATTTCGAACAACAATGTCTTGCTTGAGAAAGTTTCACTTGAAAT
129 TTTCGTTACATGATTCACGACATTTCGAACAACAACGTCTTGCTTGAGAAAGCTTCACTTGAAAT
* *
946 AGTAATTTGTCTCACTCGAGATTAAAGTAAAT
194 AGTAA--TG--TCAATCGAGATGAAAGTAAAT
**
978 CCTTCGAATCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTC-GAGTCATCTGTAAGCCT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG-GTCATCTGTAAGCCT
1042 TTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACTTCAGTGCTGGATG-TTTCAACATT
65 TTCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACTTCAGTGCTGGATGTTTTCAACATT
* * * *
1106 TTTGTTGCATGATTCACGACATTTGGAATCAACAACGTCTTGCTTTAGAAAGCTTCACTTG-AA-
130 TTCGTTACATGATTCACGACATTTCGAA-CAACAACGTCTTGCTTGAGAAAGCTTCACTTGAAAT
1169 A-T-A-G-CAATCGAGATGAAAGTAAAT
194 AGTAATGTCAATCGAGATGAAAGTAAAT
* * *
1193 CCTTTGGGTCATCAGTAAGTCTTTCGGGCATGATGATTAAATCCTTCAGGTCATCTGTAAGCCTT
1 CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTT
* ** *
1258 TCGAGCAAGATGATAAGACCATCAGGCCATCCATAAGACCTTC-G-GGTAGGATGTTTTCAA
66 TCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGA-CTTCAGTGCT-GGATGTTTTCAA
1318 TGAGATTTAA
Statistics
Matches: 307, Mismatches: 26, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
214 2 0.01
215 117 0.38
216 11 0.04
218 1 0.00
221 1 0.00
222 1 0.00
223 1 0.00
224 34 0.11
225 47 0.15
226 92 0.30
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (221 bp):
CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTT
TCGAGCAAGATGATAAGACCTTTGGGCCATCCATAAGACTTCAGTGCTGGATGTTTTCAACATTT
TCGTTACATGATTCACGACATTTCGAACAACAACGTCTTGCTTGAGAAAGCTTCACTTGAAATAG
TAATGTCAATCGAGATGAAAGTAAAT
Found at i:1245 original size:42 final size:42
Alignment explanation
Indices: 1188--1271 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1178 GAGATGAAAG
** * * *
1188 TAAATCCTTTGGGTCATCAGTAAGTCTTTCGGGCATGATGAT
1 TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATGAT
*
1230 TAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGAT
1 TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATGAT
1272 AAGACCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCAGGTCATCAGTAAGCCTTTCGAGCAAGATGAT
Found at i:1985 original size:3 final size:3
Alignment explanation
Indices: 1979--2028 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
1969 AATATTTTAA
* * *
1979 TAT TAT TAT TAT T-G TAT TCT TA- TAT TAT TAT TAA TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2024 TAT TA
1 TAT TA
2029 CAAGCCCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.13
3 33 0.87
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1985 original size:11 final size:12
Alignment explanation
Indices: 1965--2021 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 12
1955 TTTATTTTAA
*
1965 TAATAATATT-T
1 TAATATTATTAT
1976 TAATATTATTAT
1 TAATATTATTAT
*
1988 T-AT-TGTATTCT
1 TAATAT-TATTAT
1999 T-ATATTATTAT
1 TAATATTATTAT
2010 TAATATTATTAT
1 TAATATTATTAT
2022 ATTATTACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.03
11 25 0.64
12 13 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:1988 original size:14 final size:14
Alignment explanation
Indices: 1956--2028 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
1946 TTATCCCATT
*
1956 TTATTTTAATAATA
1 TTATTTTAATATTA
*
1970 ATATTTTAATATTA
1 TTATTTTAATATTA
* *
1984 TTATTATT-GTATTC
1 TTATT-TTAATATTA
* *
1998 TTATATTATTATTA
1 TTATTTTAATATTA
*
2012 ATATTATT-ATATTA
1 TTATT-TTAATATTA
2026 TTA
1 TTA
2029 CAAGCCCGAA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
13 2 0.05
14 38 0.86
15 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (14 bp):
TTATTTTAATATTA
Found at i:2826 original size:12 final size:12
Alignment explanation
Indices: 2809--2833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2799 GGAGCTGACC
2809 AAAGACTCACCT
1 AAAGACTCACCT
2821 AAAGACTCACCT
1 AAAGACTCACCT
2833 A
1 A
2834 CATGTCCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAGACTCACCT
Found at i:3640 original size:26 final size:26
Alignment explanation
Indices: 3611--3666 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3601 ACAATTACAA
3611 CATCTTAACTTCCATCACCATAAAAC
1 CATCTTAACTTCCATCACCATAAAAC
*
3637 CATCTTCACTTCCATCACCATAAAAC
1 CATCTTAACTTCCATCACCATAAAAC
3663 CATC
1 CATC
3667 CTTCAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.27
Consensus pattern (26 bp):
CATCTTAACTTCCATCACCATAAAAC
Found at i:6690 original size:27 final size:28
Alignment explanation
Indices: 6638--6702 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
6628 AAAGAAAATC
*
6638 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
6666 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
6693 AGAAAAGAAA
1 AGAAAAGAAA
6703 AGAAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:6702 original size:5 final size:5
Alignment explanation
Indices: 6692--6716 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6682 ATTCAAAAAG
6692 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
6717 GGAAAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:10673 original size:13 final size:13
Alignment explanation
Indices: 10652--10690 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
10642 TGGTCAAAGA
*
10652 TGAAGAGGTATGT
1 TGAAAAGGTATGT
10665 TGAAAAGGTATGT
1 TGAAAAGGTATGT
10678 TGAAAAGGTATGT
1 TGAAAAGGTATGT
10691 GAGAGGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:14730 original size:14 final size:14
Alignment explanation
Indices: 14711--14751 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
14701 AAGATATCAC
14711 CTTTCCATCACCAT
1 CTTTCCATCACCAT
14725 CTTTCCATCACCAT
1 CTTTCCATCACCAT
* *
14739 -TCTCTATCACCAT
1 CTTTCCATCACCAT
14752 TCACGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:14749 original size:13 final size:13
Alignment explanation
Indices: 14706--14753 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
14696 CTTATAAGAT
14706 ATCACC-TT-TCC
1 ATCACCATTCTCC
*
14717 ATCACCATCTTTCC
1 ATCACCAT-TCTCC
*
14731 ATCACCATTCTCT
1 ATCACCATTCTCC
14744 ATCACCATTC
1 ATCACCATTC
14754 ACGCCTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 6 0.19
12 1 0.03
13 14 0.44
14 11 0.34
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
ATCACCATTCTCC
Found at i:26510 original size:50 final size:50
Alignment explanation
Indices: 26451--26550 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
26441 ACCATCCCTT
26451 GTAAGACTTATAAGAAACGGGTCTTTGCTCTTTATAGCATTGGTTTTTTC
1 GTAAGACTTATAAGAAACGGGTCTTTGCTCTTTATAGCATTGGTTTTTTC
26501 GTAAGACTTATAAGAAACGGGTCTTTGCTCTTTATAGCATTGGTTTTTTC
1 GTAAGACTTATAAGAAACGGGTCTTTGCTCTTTATAGCATTGGTTTTTTC
26551 TTAGTTTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (50 bp):
GTAAGACTTATAAGAAACGGGTCTTTGCTCTTTATAGCATTGGTTTTTTC
Found at i:26643 original size:35 final size:36
Alignment explanation
Indices: 26574--26645 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
26564 ATATTATTTC
26574 CATCACCATAATCCATATTCCATTATCACGCCTATAT
1 CATCACCATAATCCATA-TCCATTATCACGCCTATAT
*
26611 CATCACCATAGTCCATCA-CCA-TATCACGCCTATAT
1 CATCACCATAATCCAT-ATCCATTATCACGCCTATAT
26646 TATTACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 14 0.42
36 3 0.09
37 15 0.45
38 1 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATAATCCATATCCATTATCACGCCTATAT
Found at i:26822 original size:15 final size:17
Alignment explanation
Indices: 26802--26835 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
26792 AACTATTTTA
26802 TCCATTTC-A-ATTCTT
1 TCCATTTCTATATTCTT
26817 TCCATTTCTATATTCTT
1 TCCATTTCTATATTCTT
26834 TC
1 TC
26836 TTTATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (17 bp):
TCCATTTCTATATTCTT
Found at i:27130 original size:14 final size:15
Alignment explanation
Indices: 27096--27142 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
27086 AATTTTGAGT
27096 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
27111 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
27125 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
27142 G
1 G
27143 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:31116 original size:35 final size:37
Alignment explanation
Indices: 31047--31126 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
31037 ATATTATTTC
*
31047 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
31084 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
31119 CATCACCA
1 CATCACCA
31127 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:33826 original size:28 final size:28
Alignment explanation
Indices: 33764--33831 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
33754 AAAGAAAATC
*
33764 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
33792 A-AGAAAGAAAATT-CAGCATTCAAAAAGA
1 AGA-AAAG-AAATTGAAGCACTCAAAAAGA
33820 AGAAAAGCAAAT
1 AGAAAAG-AAAT
33832 AAAAGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.03
28 26 0.79
29 6 0.18
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:43995 original size:17 final size:17
Alignment explanation
Indices: 43933--43985 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
43923 AATTAAGAGT
**
43933 TAGTTTAAGAAATGAAC
1 TAGTTTAATTAATGAAC
* *
43950 TAGTTTGATTTATGAAC
1 TAGTTTAATTAATGAAC
43967 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
43984 TA
1 TA
43986 ACTTTATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:44013 original size:18 final size:17
Alignment explanation
Indices: 43992--44051 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 17
43982 ACTAACTTTA
43992 TTAAATGAAATAG-ATGC
1 TTAAATGAAAT-GCATGC
*
44009 TTTAAATGCAATGCATGC
1 -TTAAATGAAATGCATGC
*
44027 TTAAATGAACT-CATGC
1 TTAAATGAAATGCATGC
44043 TTAAATGAA
1 TTAAATGAA
44052 GTAGCATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 14 0.37
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
TTAAATGAAATGCATGC
Found at i:51766 original size:11 final size:11
Alignment explanation
Indices: 51752--51807 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
51742 TCTTTTTGAA
51752 TTCTTTTTCTT
1 TTCTTTTTCTT
51763 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
51776 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
51789 TGTCTTTTTC-T
1 T-TCTTTTTCTT
51800 TTCTTTTT
1 TTCTTTTT
51808 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:51776 original size:19 final size:18
Alignment explanation
Indices: 51752--51807 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
51742 TCTTTTTGAA
51752 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
51770 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
51789 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
51807 T
1 T
51808 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:52140 original size:12 final size:12
Alignment explanation
Indices: 52123--52162 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
52113 CTGCGGAATT
52123 ATGGTCTTGATG
1 ATGGTCTTGATG
52135 ATGGTCTTGATG
1 ATGGTCTTGATG
* *
52147 AAGGATGTTGATG
1 ATGG-TCTTGATG
52160 ATG
1 ATG
52163 TTGATGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38
Consensus pattern (12 bp):
ATGGTCTTGATG
Found at i:54370 original size:18 final size:18
Alignment explanation
Indices: 54347--54381 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54337 TGGGCGAATC
54347 TAGCAAGGGTAAAGAAAG
1 TAGCAAGGGTAAAGAAAG
54365 TAGCAAGGGTAAAGAAA
1 TAGCAAGGGTAAAGAAA
54382 AGCAAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.31, T:0.11
Consensus pattern (18 bp):
TAGCAAGGGTAAAGAAAG
Found at i:59028 original size:17 final size:17
Alignment explanation
Indices: 59006--59073 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
58996 AATTAAGAGT
59006 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
59023 TAGTTTGATTTAA-GAAC
1 TAGTTT-AATAAATGAAC
*
59040 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
59057 TAACTTTATTAAATGAA
1 T-AGTTTAATAAATGAA
59074 ATAGATGCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
16 5 0.12
17 21 0.50
18 16 0.38
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:59085 original size:17 final size:16
Alignment explanation
Indices: 59065--59122 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
59055 ACTAACTTTA
59065 TTAAATGAAATAGATGC
1 TTAAATGAAAT-GATGC
*
59082 TTAAATGCAATGCATGC
1 TTAAATGAAATG-ATGC
* *
59099 TTAAATGAACTCATGC
1 TTAAATGAAATGATGC
59115 TTAAATGA
1 TTAAATGA
59123 TATAACATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
TTAAATGAAATGATGC
Done.